| Previous changeset 21:104d86c98776 (2020-03-05) Next changeset 23:c4b82dce8335 (2021-04-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d" |
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modified:
cutadapt.xml macros.xml |
| b |
| diff -r 104d86c98776 -r 093678460093 cutadapt.xml --- a/cutadapt.xml Thu Mar 05 06:45:31 2020 -0500 +++ b/cutadapt.xml Sat Jul 04 06:52:59 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="cutadapt" name="Cutadapt" version="1.16.7" profile="17.09"> +<tool id="cutadapt" name="Cutadapt" version="1.16.8" profile="17.09"> <description>Remove adapter sequences from Fastq/Fasta</description> <macros> <import>macros.xml</import> @@ -113,7 +113,7 @@ #if str($filter_options.max): --maximum-length=$filter_options.max #end if -#if $filter_options.max_n: +#if str($filter_options.max_n): --max-n=$filter_options.max_n #end if #if str( $library.type ) != "single": @@ -131,16 +131,16 @@ #end if $read_mod_options.trim_n #if $read_mod_options.prefix != '': - --prefix="$read_mod_options.prefix" + --prefix='$read_mod_options.prefix' #end if #if $read_mod_options.suffix != '': - --suffix="$read_mod_options.suffix" + --suffix='$read_mod_options.suffix' #end if #if str($read_mod_options.length) != '0': --length=$read_mod_options.length #end if #if $read_mod_options.length_tag != '': - --length-tag="$read_mod_options.length_tag" + --length-tag='$read_mod_options.length_tag' #end if '${read1}' @@ -518,14 +518,14 @@ <param name="discard_untrimmed" value="true"/> <param name="min" value="1"/> <param name="max" value="1000"/> - <param name="max_n" value="1"/> + <param name="max_n" value="0"/> <param name="pair_filter" value="both"/> </section> <assert_command> <has_text text="--discard-untrimmed"/> <has_text text="--minimum-length=1"/> <has_text text="--maximum-length=1000"/> - <has_text text="--max-n=1"/> + <has_text text="--max-n=0"/> <has_text text="--pair-filter=both"/> </assert_command> </test> |
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| diff -r 104d86c98776 -r 093678460093 macros.xml --- a/macros.xml Thu Mar 05 06:45:31 2020 -0500 +++ b/macros.xml Sat Jul 04 06:52:59 2020 -0400 |
| b |
| b'@@ -6,7 +6,7 @@\n \n #for $a in $library.r1.adapters\n #if $a.adapter_source.adapter_source_list == \'builtin\':\n- -a "${a.adapter_source.adapter.fields.name}"=\'${a.adapter_source.adapter}\'\n+ -a \'${a.adapter_source.adapter.fields.name}\'=\'${a.adapter_source.adapter}\'\n #else if $a.adapter_source.adapter_source_list == \'file\':\n -a file:\'${a.adapter_source.adapter_file}\'\n #else if str($a.adapter_source.adapter_name) != "":\n@@ -17,7 +17,7 @@\n #end for\n #for $aa in $library.r1.anywhere_adapters\n #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == \'builtin\':\n- -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n+ -b \'${aa.anywhere_adapter_source.anywhere_adapter.fields.name}\'=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == \'file\':\n -b file:\'${aa.anywhere_adapter_source.anywhere_adapter_file}\'\n #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":\n@@ -28,7 +28,7 @@\n #end for\n #for $fa in $library.r1.front_adapters\n #if $fa.front_adapter_source.front_adapter_source_list == \'builtin\':\n- -g "${fa.front_adapter_source.front_adapter.fields.name}"=\'${fa.front_adapter_source.front_adapter}\'\n+ -g \'${fa.front_adapter_source.front_adapter.fields.name}\'=\'${fa.front_adapter_source.front_adapter}\'\n #else if $fa.front_adapter_source.front_adapter_source_list == \'file\':\n -g file:\'${fa.front_adapter_source.front_adapter_file}\'\n #else if str($fa.front_adapter_source.front_adapter_name) != "":\n@@ -71,7 +71,7 @@\n \n #for $a in $library.r2.adapters2\n #if $a.adapter_source2.adapter_source_list2 == \'builtin\':\n- -A "${a.adapter_source2.adapter2.fields.name}"=\'${a.adapter_source2.adapter2}\'\n+ -A \'${a.adapter_source2.adapter2.fields.name}\'=\'${a.adapter_source2.adapter2}\'\n #else if $a.adapter_source2.adapter_source_list2 == \'file\':\n -A file:\'${a.adapter_source2.adapter_file2}\'\n #else if str($a.adapter_source2.adapter_name2) != "":\n@@ -82,7 +82,7 @@\n #end for\n #for $aa in $library.r2.anywhere_adapters2\n #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == \'builtin\':\n- -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"=\'${aa.anywhere_adapter_source2.anywhere_adapter2}\'\n+ -B \'${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}\'=\'${aa.anywhere_adapter_source2.anywhere_adapter2}\'\n #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == \'file\':\n -B file:\'${aa.anywhere_adapter_source2.anywhere_adapter_file2}\'\n #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":\n@@ -93,7 +93,7 @@\n #end for\n #for $fa in $library.r2.front_adapters2\n #if $fa.front_adapter_source2.front_adapter_source_list2 == \'builtin\':\n- -G "${fa.front_adapter_source2.front_adapter2.fields.name}"=\'${fa.front_adapter_source2.front_adapter2}\'\n+ -G \'${fa.front_adapter_source2.front_adapter2.fields.name}\'=\'${fa.front_adapter_source2.front_adapter2}\'\n #else if $fa.front_adapter_source2.front_adapter_source_list2 == \'file\':\n -G file:\'${fa.front_adapter_source2.front_adapter_file2}\'\n #else if str($fa.front_adapter_source2.front_adapter_name2) != "":\n@@ -121,6 +121,57 @@\n \n ]]></token>\n \n+ <xml name="adapter_sanitizer">\n+ <sanitizer>\n+ <valid initial="string.digits">\n+ <add value="A"/><!--standard nucleotides-->\n+ <add value="T"/>\n+ '..b'\n \n <when value="user">\n <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3\' adapter name (Optional)" />\n- <param name="adapter2" argument="-A" type="text" label="Enter custom 3\' adapter sequence" value="AATTGGCC" />\n+ <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3\' adapter sequence" value="AATTGGCC" />\n </when>\n \n <when value="builtin">\n- <param name="adapter2" argument="-A" type="select" label="Choose 3\' adapter">\n- <options from_data_table="adapters">\n- <filter type="sort_by" column="1" />\n- </options>\n- </param>\n+ <expand macro="adapter_select" name="adapter2" argument="-A" label="Choose 3\' adapter"/>\n </when>\n <when value="file">\n <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3\' adapters" />\n@@ -252,14 +287,10 @@\n \n <when value="user">\n <param name="front_adapter_name2" type="text" value="" label="Enter custom 5\' adapter name (Optional)" />\n- <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5\' adapter sequence" />\n+ <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5\' adapter sequence" />\n </when>\n <when value="builtin">\n- <param name="front_adapter2" argument="-G" type="select" label="Choose 5\' adapter">\n- <options from_data_table="adapters">\n- <filter type="sort_by" column="1" />\n- </options>\n- </param>\n+ <expand macro="adapter_select" name="front_adapter2" argument="-G" label="Choose 5\' adapter"/>\n </when>\n <when value="file">\n <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5\' adapters" />\n@@ -277,14 +308,10 @@\n \n <when value="user">\n <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5\' or 3\' adapter name (Optional)" />\n- <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5\' or 3\' adapter sequence" value="AATTGGCC" />\n+ <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5\' or 3\' adapter sequence" value="AATTGGCC" />\n </when>\n <when value="builtin">\n- <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5\' or 3\' adapter">\n- <options from_data_table="adapters">\n- <filter type="sort_by" column="1" />\n- </options>\n- </param>\n+ <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5\' or 3\' adapter"/>\n </when>\n <when value="file">\n <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3\' or 5\' adapters" />\n' |